Low salt Vs Control
jeff karnsomprot
2025-06-29
1 Loading in Data sets + Library packages.
##
## The downloaded binary packages are in
## /var/folders/7n/x74qctp91rng390gx0z9hmd80000gn/T//RtmppF2EYo/downloaded_packages2 Loading Dataset
options(future.globals.maxSize = 74 * 1024^3) # 55 GB
getOption("future.globals.maxSize") #59055800320## [1] 79456894976Idents(SO4) <- "subclass2_MD"
SO4$sample <- factor(SO4$sample, levels = c("SO1", "SO4", "SO3", "SO2"))
VlnPlot(SO4,"S100g",split.by = "treatment",group.by = "sample")## The default behaviour of split.by has changed.
## Separate violin plots are now plotted side-by-side.
## To restore the old behaviour of a single split violin,
## set split.plot = TRUE.
##
## This message will be shown once per session.## Warning: The `slot` argument of `FetchData()` is deprecated as of SeuratObject 5.0.0.
## ℹ Please use the `layer` argument instead.
## ℹ The deprecated feature was likely used in the Seurat package.
## Please report the issue at <https://github.com/satijalab/seurat/issues>.
## This warning is displayed once every 8 hours.
## Call `lifecycle::last_lifecycle_warnings()` to see where this warning was
## generated.## Warning: `PackageCheck()` was deprecated in SeuratObject 5.0.0.
## ℹ Please use `rlang::check_installed()` instead.
## ℹ The deprecated feature was likely used in the Seurat package.
## Please report the issue at <https://github.com/satijalab/seurat/issues>.
## This warning is displayed once every 8 hours.
## Call `lifecycle::last_lifecycle_warnings()` to see where this warning was
## generated.
# Macula Densa Markers , Nos1, Avpr1a, Slc12a1, Ptgs2, and Slc9a2
VlnPlot(SO4, c("Nos1","Avpr1a","Slc12a1","Ptgs2","Slc9a2","Pappa2"),split.by = "treatment",group.by = "treatment")
## Warning: The following arguments are not used: drop
3 Markers of control vs low_salt up/down regulation
Upregulated = low salt, positive, activated by low_salt Downregulated = control, negative, supressed of low_salt
Idents(SO4) <- "treatment"
type_markers <- FindMarkers(
object = SO4,
ident.1 = "low_salt",
ident.2 = "control",
group.by = "treatment",
min.pct = 0.1,
logfc.threshold = 0.1,
only.pos = FALSE
)## Warning: The `slot` argument of `GetAssayData()` is deprecated as of SeuratObject 5.0.0.
## ℹ Please use the `layer` argument instead.
## ℹ The deprecated feature was likely used in the Seurat package.
## Please report the issue at <https://github.com/satijalab/seurat/issues>.
## This warning is displayed once every 8 hours.
## Call `lifecycle::last_lifecycle_warnings()` to see where this warning was
## generated.## For a (much!) faster implementation of the Wilcoxon Rank Sum Test,
## (default method for FindMarkers) please install the presto package
## --------------------------------------------
## install.packages('devtools')
## devtools::install_github('immunogenomics/presto')
## --------------------------------------------
## After installation of presto, Seurat will automatically use the more
## efficient implementation (no further action necessary).
## This message will be shown once per session type_markers$gene <- rownames(type_markers)
type_markers <-type_markers %>% arrange(desc(avg_log2FC))3.1 Pathway Upregulated = Low salt
df<- type_markers
df2 <- df %>% filter(p_val_adj < 0.05)
DEG_list <- df2
markers1up <- DEG_list %>% rownames_to_column(var="SYMBOL")
ENTREZ_list <- bitr(
geneID = rownames(DEG_list),
fromType = "SYMBOL",
toType = "ENTREZID",
OrgDb = org.Mm.eg.db
)## 'select()' returned 1:1 mapping between keys and columns## Warning in bitr(geneID = rownames(DEG_list), fromType = "SYMBOL", toType =
## "ENTREZID", : 2.76% of input gene IDs are fail to map...markers1up <- ENTREZ_list %>% inner_join(markers1up, by = "SYMBOL")
markers1up <- markers1up %>% dplyr::filter(p_val_adj < 0.05)
#head(markers, n = 50)
pos.markers1up <- markers1up %>% dplyr::filter(avg_log2FC > 0.4) %>% arrange(desc(abs(avg_log2FC)))
#change around avg log value
pos.ranks1up <- pos.markers1up$ENTREZID[abs(pos.markers1up$avg_log2FC) > 0]
#head(pos.ranks)
pos_go1up <- enrichGO(gene = pos.ranks1up, #a vector of entrez gene id
OrgDb = "org.Mm.eg.db",
ont = "BP",
readable = TRUE) #whether mapping gene ID to gene Name
pos_go1up## #
## # over-representation test
## #
## #...@organism Mus musculus
## #...@ontology BP
## #...@keytype ENTREZID
## #...@gene chr [1:131] "16010" "239435" "23850" "19283" "66815" "19225" "70337" ...
## #...pvalues adjusted by 'BH' with cutoff <0.05
## #...417 enriched terms found
## 'data.frame': 417 obs. of 12 variables:
## $ ID : chr "GO:0010563" "GO:0045936" "GO:0042326" "GO:0031400" ...
## $ Description : chr "negative regulation of phosphorus metabolic process" "negative regulation of phosphate metabolic process" "negative regulation of phosphorylation" "negative regulation of protein modification process" ...
## $ GeneRatio : chr "16/125" "16/125" "14/125" "15/125" ...
## $ BgRatio : chr "388/28928" "388/28928" "337/28928" "420/28928" ...
## $ RichFactor : num 0.0412 0.0412 0.0415 0.0357 0.0411 ...
## $ FoldEnrichment: num 9.54 9.54 9.61 8.27 9.52 ...
## $ zScore : num 11.16 11.16 10.48 9.88 10.03 ...
## $ pvalue : num 1.33e-11 1.33e-11 2.48e-10 4.44e-10 1.26e-09 ...
## $ p.adjust : num 1.84e-08 1.84e-08 2.28e-07 3.06e-07 6.97e-07 ...
## $ qvalue : num 1.29e-08 1.29e-08 1.60e-07 2.15e-07 4.89e-07 ...
## $ geneID : chr "Hspb1/Cep85/Dusp1/Cdkn1c/Bmp2/Rgs2/Aldob/Cdk5rap1/Spry1/Jun/Ier3/Sh3bp5/Irf1/Gstp1/Dynll1/Ppp1r15a" "Hspb1/Cep85/Dusp1/Cdkn1c/Bmp2/Rgs2/Aldob/Cdk5rap1/Spry1/Jun/Ier3/Sh3bp5/Irf1/Gstp1/Dynll1/Ppp1r15a" "Hspb1/Cep85/Dusp1/Cdkn1c/Bmp2/Rgs2/Cdk5rap1/Spry1/Jun/Sh3bp5/Irf1/Gstp1/Dynll1/Ppp1r15a" "Hspb1/Cep85/Dusp1/Cdkn1c/Bmp2/Rgs2/Cdk5rap1/Hspa1b/Spry1/Jun/Sh3bp5/Irf1/Gstp1/Bex2/Ppp1r15a" ...
## $ Count : int 16 16 14 15 13 11 10 10 5 10 ...
## #...Citation
## G Yu. Thirteen years of clusterProfiler. The Innovation. 2024, 5(6):100722 chart1up <- dotplot(pos_go1up) +
ggtitle("upregulated lowsalt") +
theme_classic() +
theme(
plot.title = element_text(hjust = 0.5),
legend.position = "left",
axis.text.y = element_text(hjust = 0, size = 10)) +
scale_y_discrete(position = "right",
labels = function(x) str_wrap(x, width = 25)) # Wrap y-axis labels to 2 lines## Scale for y is already present.
## Adding another scale for y, which will replace the existing scale.
### Upregulation Gene View
pathway_type1up <- strsplit(pos_go1up$geneID, "/")
names(pathway_type1up) <- pos_go1up$Description
pathway_type1up## $`negative regulation of phosphorus metabolic process`
## [1] "Hspb1" "Cep85" "Dusp1" "Cdkn1c" "Bmp2" "Rgs2"
## [7] "Aldob" "Cdk5rap1" "Spry1" "Jun" "Ier3" "Sh3bp5"
## [13] "Irf1" "Gstp1" "Dynll1" "Ppp1r15a"
##
## $`negative regulation of phosphate metabolic process`
## [1] "Hspb1" "Cep85" "Dusp1" "Cdkn1c" "Bmp2" "Rgs2"
## [7] "Aldob" "Cdk5rap1" "Spry1" "Jun" "Ier3" "Sh3bp5"
## [13] "Irf1" "Gstp1" "Dynll1" "Ppp1r15a"
##
## $`negative regulation of phosphorylation`
## [1] "Hspb1" "Cep85" "Dusp1" "Cdkn1c" "Bmp2" "Rgs2"
## [7] "Cdk5rap1" "Spry1" "Jun" "Sh3bp5" "Irf1" "Gstp1"
## [13] "Dynll1" "Ppp1r15a"
##
## $`negative regulation of protein modification process`
## [1] "Hspb1" "Cep85" "Dusp1" "Cdkn1c" "Bmp2" "Rgs2"
## [7] "Cdk5rap1" "Hspa1b" "Spry1" "Jun" "Sh3bp5" "Irf1"
## [13] "Gstp1" "Bex2" "Ppp1r15a"
##
## $`negative regulation of protein phosphorylation`
## [1] "Hspb1" "Cep85" "Dusp1" "Cdkn1c" "Bmp2" "Rgs2"
## [7] "Cdk5rap1" "Spry1" "Jun" "Sh3bp5" "Irf1" "Gstp1"
## [13] "Ppp1r15a"
##
## $`negative regulation of transferase activity`
## [1] "Hspb1" "Cep85" "Dusp1" "Cdkn1c" "Bmp2" "Rgs2"
## [7] "Cdk5rap1" "Zfp36" "Spry1" "Sh3bp5" "Gstp1"
##
## $`negative regulation of protein kinase activity`
## [1] "Hspb1" "Cep85" "Dusp1" "Cdkn1c" "Bmp2" "Rgs2"
## [7] "Cdk5rap1" "Spry1" "Sh3bp5" "Gstp1"
##
## $`negative regulation of kinase activity`
## [1] "Hspb1" "Cep85" "Dusp1" "Cdkn1c" "Bmp2" "Rgs2"
## [7] "Cdk5rap1" "Spry1" "Sh3bp5" "Gstp1"
##
## $`protein refolding`
## [1] "Hspb1" "Hspa1a" "Hspa1b" "Hspa8" "Hspa5"
##
## $`cellular response to transforming growth factor beta stimulus`
## [1] "Fos" "Cdkn1c" "Cav2" "Bmp2" "Bambi" "Wnt10a" "Spry1" "Jun"
## [9] "Hspa5" "Cited1"
##
## $`transforming growth factor beta receptor signaling pathway`
## [1] "Fos" "Cdkn1c" "Cav2" "Bmp2" "Bambi" "Spry1" "Jun" "Hspa5"
## [9] "Cited1"
##
## $`response to transforming growth factor beta`
## [1] "Fos" "Cdkn1c" "Cav2" "Bmp2" "Bambi" "Wnt10a" "Spry1" "Jun"
## [9] "Hspa5" "Cited1"
##
## $`chaperone-mediated protein folding`
## [1] "Hspb1" "Hspa1a" "Hspa1b" "Hspa8" "Hspa5" "Clu"
##
## $`transforming growth factor beta receptor superfamily signaling pathway`
## [1] "Fos" "Cdkn1c" "Cav2" "Bmp2" "Bambi" "Spry1" "Hfe" "Bmper"
## [9] "Jun" "Hspa5" "Cited1"
##
## $`positive regulation of cell projection organization`
## [1] "Ptprz1" "Ache" "Hspb1" "Rgs2" "Scarf1" "Hap1" "Dynlt1f"
## [8] "Lcn2" "Dynll1" "Hspa5" "Robo2" "Cx3cl1"
##
## $`regulation of epithelial cell differentiation`
## [1] "Cdkn1c" "Etv4" "Bmp2" "Sfn" "Zfp36" "F11r" "Spry1" "Cited1"
##
## $`cell surface receptor protein serine/threonine kinase signaling pathway`
## [1] "Fos" "Cdkn1c" "Cav2" "Bmp2" "Bambi" "Spry1" "Hfe" "Bmper"
## [9] "Jun" "Hspa5" "Cited1"
##
## $`negative regulation of cell adhesion`
## [1] "Ptprz1" "Hspb1" "Dusp1" "Bcl6" "Bmp2" "Hfe" "Irf1" "Gstp1"
## [9] "Arg2" "Acer2"
##
## $`negative regulation of MAP kinase activity`
## [1] "Dusp1" "Bmp2" "Rgs2" "Spry1" "Gstp1"
##
## $`SMAD protein signal transduction`
## [1] "Fos" "Bmp2" "Hfe" "Bmper" "Jun" "Cited1"
##
## $`negative regulation of protein serine/threonine kinase activity`
## [1] "Dusp1" "Bmp2" "Rgs2" "Cdk5rap1" "Spry1" "Gstp1"
##
## $`negative regulation of neuron apoptotic process`
## [1] "Ptprz1" "Btg2" "Jun" "Lcn2" "Cited1" "Tox3" "Clu" "Cx3cl1"
##
## $`response to metal ion`
## [1] "Ptgs2" "Fos" "Junb" "Chp2" "Aldob" "Hspa8" "Hfe"
## [8] "Jun" "Trpc1" "Pla2g4a"
##
## $regeneration
## [1] "Mcub" "Scarf1" "Hfe" "Mymx" "Jun" "Cspg5" "Gstp1" "Cpq"
##
## $`prostaglandin transport`
## [1] "Ptgs2" "Ptges" "Pla2g4a" "Slco4a1"
##
## $`ureteric bud development`
## [1] "Bmp2" "Spry1" "Bmper" "Arg2" "Cited1" "Robo2"
##
## $`regulation of protein kinase activity`
## [1] "Hspb1" "Cep85" "Dusp1" "Cdkn1c" "Bmp2" "Sfn"
## [7] "Rgs2" "Cdk5rap1" "Spry1" "Sh3bp5" "Gstp1"
##
## $`positive regulation of neuron projection development`
## [1] "Ptprz1" "Hspb1" "Rgs2" "Scarf1" "Hap1" "Dynlt1f" "Hspa5"
## [8] "Cx3cl1"
##
## $`mesonephric epithelium development`
## [1] "Bmp2" "Spry1" "Bmper" "Arg2" "Cited1" "Robo2"
##
## $`mesonephric tubule development`
## [1] "Bmp2" "Spry1" "Bmper" "Arg2" "Cited1" "Robo2"
##
## $`chaperone cofactor-dependent protein refolding`
## [1] "Hspa1a" "Hspa1b" "Hspa8" "Hspa5"
##
## $`mesonephros development`
## [1] "Bmp2" "Spry1" "Bmper" "Arg2" "Cited1" "Robo2"
##
## $`regulation of transmembrane receptor protein serine/threonine kinase signaling pathway`
## [1] "Cdkn1c" "Cav2" "Bmp2" "Bambi" "Spry1" "Hfe" "Bmper" "Hspa5"
##
## $`osteoclast differentiation`
## [1] "Fos" "Junb" "Bmp2" "Klf10" "Anxa2" "Mafb"
##
## $`response to topologically incorrect protein`
## [1] "Hspb1" "Hspa1a" "Manf" "Hspa5" "Ppp1r15a" "Clu"
##
## $`cellular response to metal ion`
## [1] "Ptgs2" "Fos" "Junb" "Chp2" "Hspa8" "Hfe" "Jun"
##
## $`regulation of hemopoiesis`
## [1] "Hspb1" "Fos" "Bcl6" "Cd83" "Hspa1b" "Zfp36" "Klf10" "Jun"
## [9] "Irf1" "Mafb"
##
## $`negative regulation of type 2 immune response`
## [1] "Bcl6" "Irf1" "Arg2"
##
## $`regulation of vesicle fusion`
## [1] "Syt5" "Pla2g4a" "Rab3a" "Anxa2"
##
## $`'de novo' post-translational protein folding`
## [1] "Hspa1a" "Hspa1b" "Hspa8" "Hspa5"
##
## $`regulation of transforming growth factor beta receptor signaling pathway`
## [1] "Cdkn1c" "Cav2" "Bmp2" "Bambi" "Spry1" "Hspa5"
##
## $`'de novo' protein folding`
## [1] "Hspa1a" "Hspa1b" "Hspa8" "Hspa5"
##
## $`response to calcium ion`
## [1] "Fos" "Junb" "Chp2" "Jun" "Trpc1" "Pla2g4a"
##
## $`negative regulation of cell-cell adhesion`
## [1] "Hspb1" "Bcl6" "Bmp2" "Hfe" "Irf1" "Gstp1" "Arg2"
##
## $`regulation of cellular response to transforming growth factor beta stimulus`
## [1] "Cdkn1c" "Cav2" "Bmp2" "Bambi" "Spry1" "Hspa5"
##
## $`negative regulation of transmembrane receptor protein serine/threonine kinase signaling pathway`
## [1] "Cav2" "Bmp2" "Bambi" "Spry1" "Bmper" "Hspa5"
##
## $`response to heat`
## [1] "Ptgs2" "Hspb1" "Hspa1a" "Hspa1b" "Hspa8"
##
## $`response to tumor necrosis factor`
## [1] "Ptgs2" "Fos" "Hspa1b" "Zfp36" "Traf1" "Irf1" "Cx3cl1"
##
## $`female pregnancy`
## [1] "Ptgs2" "Fos" "Junb" "Rgs2" "Hfe" "Pla2g4a" "Hsd11b2"
##
## $`negative regulation of alpha-beta T cell activation`
## [1] "Bcl6" "Hfe" "Irf1" "Arg2"
##
## $`negative regulation of leukocyte cell-cell adhesion`
## [1] "Hspb1" "Bcl6" "Hfe" "Irf1" "Gstp1" "Arg2"
##
## $`negative regulation of transforming growth factor beta receptor signaling pathway`
## [1] "Cav2" "Bmp2" "Bambi" "Spry1" "Hspa5"
##
## $`response to starvation`
## [1] "Fos" "Zfp36" "Hspa8" "Hfe" "Klf10" "Jun" "Hspa5"
##
## $`prostaglandin secretion`
## [1] "Ptgs2" "Ptges" "Pla2g4a"
##
## $`regulation of inclusion body assembly`
## [1] "Hspa1b" "Hap1" "Clu"
##
## $`regulation of neuron apoptotic process`
## [1] "Ptprz1" "Btg2" "Jun" "Lcn2" "Cited1" "Tox3" "Clu" "Cx3cl1"
##
## $`negative regulation of response to external stimulus`
## [1] "Dusp1" "Sfn" "Zfp36" "Ier3" "Gstp1" "Arg2" "Robo2" "Anxa2"
## [9] "Cx3cl1"
##
## $`kidney epithelium development`
## [1] "Bmp2" "Spry1" "Bmper" "Arg2" "Cited1" "Robo2"
##
## $`regulation of acute inflammatory response`
## [1] "Ptgs2" "Ptges" "C2cd4b" "Gstp1"
##
## $`plasma membrane organization`
## [1] "Cav2" "Mymx" "Rab3a" "Clu" "Anxa2" "Mafb"
##
## $`negative regulation of apoptotic signaling pathway`
## [1] "Ptgs2" "Hspb1" "Hspa1b" "Ier3" "Gstp1" "Clu" "Cx3cl1"
##
## $`multi-organism reproductive process`
## [1] "Ptgs2" "Fos" "Junb" "Rgs2" "Hfe" "Pla2g4a" "Hsd11b2"
##
## $`macrophage activation`
## [1] "Mcub" "Jun" "Pla2g4a" "Clu" "Cx3cl1"
##
## $`protein folding`
## [1] "Hspb1" "Hspa1a" "Hspa1b" "Hspa8" "Hspa5" "Clu"
##
## $`multi-multicellular organism process`
## [1] "Ptgs2" "Fos" "Junb" "Rgs2" "Hfe" "Pla2g4a" "Hsd11b2"
##
## $`response to steroid hormone`
## [1] "Ptgs2" "Fos" "Junb" "Zfp36" "Hspa8" "Jun" "Gstp1"
## [8] "Hsd11b2"
##
## $`regulation of protein serine/threonine kinase activity`
## [1] "Dusp1" "Bmp2" "Sfn" "Rgs2" "Cdk5rap1" "Spry1" "Gstp1"
##
## $`response to unfolded protein`
## [1] "Hspb1" "Hspa1a" "Manf" "Hspa5" "Ppp1r15a"
##
## $`membrane fusion`
## [1] "Syt5" "Cav2" "Mymx" "Pla2g4a" "Rab3a" "Anxa2"
##
## $`prostaglandin metabolic process`
## [1] "Ptgs2" "Ptges" "Pla2g4a" "Gstp1"
##
## $`prostanoid metabolic process`
## [1] "Ptgs2" "Ptges" "Pla2g4a" "Gstp1"
##
## $`organ induction`
## [1] "Bmp2" "Spry1" "Robo2"
##
## $`acute inflammatory response`
## [1] "Ptgs2" "Ptges" "C2cd4b" "Hfe" "Gstp1"
##
## $`regulation of lipid localization`
## [1] "Ptges" "Lipg" "Vstm2a" "Pla2g4a" "Anxa2" "Ttc39b"
##
## $`regulation of leukocyte differentiation`
## [1] "Hspb1" "Fos" "Bcl6" "Cd83" "Klf10" "Jun" "Irf1" "Mafb"
##
## $`maternal process involved in female pregnancy`
## [1] "Ptgs2" "Junb" "Rgs2" "Pla2g4a"
##
## $`regulation of alpha-beta T cell activation`
## [1] "Bcl6" "Cd83" "Hfe" "Irf1" "Arg2"
##
## $`positive regulation of lipid localization`
## [1] "Ptges" "Lipg" "Vstm2a" "Pla2g4a" "Anxa2"
##
## $`kidney development`
## [1] "Cdkn1c" "Bmp2" "Spry1" "Hspa8" "Bmper" "Arg2" "Cited1" "Robo2"
##
## $`regulation of tumor necrosis factor production`
## [1] "Hspb1" "Zfp36" "Gstp1" "Arg2" "Clu" "Cx3cl1"
##
## $`regulation of tumor necrosis factor superfamily cytokine production`
## [1] "Hspb1" "Zfp36" "Gstp1" "Arg2" "Clu" "Cx3cl1"
##
## $`icosanoid transport`
## [1] "Ptgs2" "Ptges" "Pla2g4a" "Slco4a1"
##
## $`positive regulation of vesicle fusion`
## [1] "Syt5" "Pla2g4a" "Anxa2"
##
## $`negative regulation of muscle contraction`
## [1] "Ptgs2" "Rgs2" "Arg2"
##
## $`negative regulation of leukocyte activation`
## [1] "Hspb1" "Bcl6" "Hfe" "Irf1" "Arg2" "Cx3cl1"
##
## $`positive regulation of fat cell differentiation`
## [1] "Ptgs2" "Bmp2" "Zfp36" "Vstm2a"
##
## $`tumor necrosis factor production`
## [1] "Hspb1" "Zfp36" "Gstp1" "Arg2" "Clu" "Cx3cl1"
##
## $`myeloid leukocyte differentiation`
## [1] "Fos" "Junb" "Bmp2" "Klf10" "Jun" "Anxa2" "Mafb"
##
## $`muscle cell proliferation`
## [1] "Ptgs2" "Fos" "Cav2" "Bmp2" "Jun" "Gstp1" "Cx3cl1"
##
## $`cellular response to tumor necrosis factor`
## [1] "Fos" "Hspa1b" "Zfp36" "Traf1" "Irf1" "Cx3cl1"
##
## $`tumor necrosis factor superfamily cytokine production`
## [1] "Hspb1" "Zfp36" "Gstp1" "Arg2" "Clu" "Cx3cl1"
##
## $`renal system development`
## [1] "Cdkn1c" "Bmp2" "Spry1" "Hspa8" "Bmper" "Arg2" "Cited1" "Robo2"
##
## $`inclusion body assembly`
## [1] "Hspa1b" "Hap1" "Clu"
##
## $`vesicle fusion`
## [1] "Syt5" "Cav2" "Pla2g4a" "Rab3a" "Anxa2"
##
## $`regulation of membrane permeability`
## [1] "F11r" "Hspa8" "Dynlt1f" "Ier3"
##
## $`neuron apoptotic process`
## [1] "Ptprz1" "Btg2" "Jun" "Lcn2" "Cited1" "Tox3" "Clu" "Cx3cl1"
##
## $`phenol-containing compound metabolic process`
## [1] "Iyd" "Trpc1" "Slco4a1" "Cited1" "Cpq"
##
## $`organelle membrane fusion`
## [1] "Syt5" "Cav2" "Pla2g4a" "Rab3a" "Anxa2"
##
## $`positive regulation of secretion by cell`
## [1] "Ptges" "Bmp2" "Hfe" "Trpc1" "Pla2g4a" "Dynll1" "Rab3a"
## [8] "Anxa2"
##
## $`prostaglandin biosynthetic process`
## [1] "Ptgs2" "Ptges" "Pla2g4a"
##
## $`regulation of animal organ formation`
## [1] "Bmp2" "Spry1" "Robo2"
##
## $`prostanoid biosynthetic process`
## [1] "Ptgs2" "Ptges" "Pla2g4a"
##
## $`cellular response to cadmium ion`
## [1] "Fos" "Hspa8" "Jun"
##
## $`positive regulation of protein binding`
## [1] "Bmp2" "Bambi" "Hfe" "Anxa2"
##
## $`regulation of inflammatory response`
## [1] "Ptgs2" "Ptges" "Bcl6" "Zfp36" "C2cd4b" "Ier3" "Gstp1" "Cx3cl1"
##
## $decidualization
## [1] "Ptgs2" "Junb" "Pla2g4a"
##
## $`regulation of supramolecular fiber organization`
## [1] "Hspa1a" "Hspa1b" "F11r" "Limch1" "Hspa8" "Capg" "Clu" "Cx3cl1"
##
## $`negative regulation of T cell activation`
## [1] "Hspb1" "Bcl6" "Hfe" "Irf1" "Arg2"
##
## $`positive regulation of leukocyte differentiation`
## [1] "Fos" "Bcl6" "Cd83" "Klf10" "Jun" "Irf1"
##
## $`positive regulation of hemopoiesis`
## [1] "Fos" "Bcl6" "Cd83" "Klf10" "Jun" "Irf1"
##
## $`regulation of type 2 immune response`
## [1] "Bcl6" "Irf1" "Arg2"
##
## $`response to reactive oxygen species`
## [1] "Fos" "Rhob" "Hspa8" "Jun" "Lcn2" "Gstp1"
##
## $`negative regulation of cell activation`
## [1] "Hspb1" "Bcl6" "Hfe" "Irf1" "Arg2" "Cx3cl1"
##
## $`negative regulation of cytokine production`
## [1] "Bcl6" "Cd83" "Zfp36" "Hfe" "Gstp1" "Arg2" "Cx3cl1"
##
## $`regulation of response to endoplasmic reticulum stress`
## [1] "Manf" "Hspa5" "Ppp1r15a" "Clu"
##
## $dephosphorylation
## [1] "Ptprz1" "Dusp1" "Chp2" "Bmp2" "Ppm1j" "Ppp1r15a"
##
## $`cellular response to calcium ion`
## [1] "Fos" "Junb" "Chp2" "Jun"
##
## $`response to toxic substance`
## [1] "Ptgs2" "Fos" "Ptges" "Pon2" "Lcn2" "Gstp1"
##
## $`regulation of myeloid cell differentiation`
## [1] "Fos" "Hspa1b" "Zfp36" "Klf10" "Jun" "Mafb"
##
## $`regulation of CD4-positive, alpha-beta T cell activation`
## [1] "Bcl6" "Cd83" "Irf1" "Arg2"
##
## $`regulation of lipid transport`
## [1] "Ptges" "Lipg" "Pla2g4a" "Anxa2" "Ttc39b"
##
## $`response to oxidative stress`
## [1] "Ptgs2" "Hspb1" "Fos" "Rhob" "Hspa8" "Jun" "Lcn2" "Gstp1"
##
## $`leukocyte cell-cell adhesion`
## [1] "Hspb1" "Bcl6" "Cd83" "F11r" "Hfe" "Irf1" "Gstp1" "Arg2"
##
## $`skeletal muscle organ development`
## [1] "Mcub" "Fos" "Btg2" "Cav2" "Hspa8" "Mymx"
##
## $`regulation of cellular response to growth factor stimulus`
## [1] "Cdkn1c" "Cav2" "Bmp2" "Bambi" "Spry1" "Bmper" "Hspa5"
##
## $`osteoblast differentiation`
## [1] "Ache" "Junb" "Bmp2" "Tent5a" "Bambi" "Cited1"
##
## $`neuroinflammatory response`
## [1] "Ptgs2" "Jun" "Clu" "Cx3cl1"
##
## $`cellular response to reactive oxygen species`
## [1] "Fos" "Rhob" "Hspa8" "Jun" "Lcn2"
##
## $`thyroid hormone metabolic process`
## [1] "Iyd" "Slco4a1" "Cpq"
##
## $`response to interleukin-4`
## [1] "Mcm2" "Hspa5" "Cited1"
##
## $`negative regulation of CD4-positive, alpha-beta T cell activation`
## [1] "Bcl6" "Irf1" "Arg2"
##
## $`regulation of MAP kinase activity`
## [1] "Dusp1" "Bmp2" "Rgs2" "Spry1" "Gstp1"
##
## $`response to glucocorticoid`
## [1] "Ptgs2" "Fos" "Zfp36" "Gstp1" "Hsd11b2"
##
## $`regulation of metal ion transport`
## [1] "Mcub" "Ptgs2" "Hfe" "Hap1" "Trpc1" "Lcn2" "Cacna2d1"
## [8] "Cx3cl1"
##
## $`regulation of apoptotic signaling pathway`
## [1] "Ptgs2" "Hspb1" "Hspa1b" "Traf1" "Ier3" "Gstp1" "Clu" "Cx3cl1"
##
## $`specification of animal organ identity`
## [1] "Bmp2" "Spry1" "Robo2"
##
## $`developmental induction`
## [1] "Bmp2" "Spry1" "Robo2"
##
## $`positive regulation of SMAD protein signal transduction`
## [1] "Bmp2" "Hfe" "Bmper"
##
## $`positive regulation of animal organ morphogenesis`
## [1] "Bmp2" "Spry1" "Robo2"
##
## $`fatty acid biosynthetic process`
## [1] "Ptgs2" "Ptges" "Lipg" "Pla2g4a" "Gstp1"
##
## $`positive regulation of secretion`
## [1] "Ptges" "Bmp2" "Hfe" "Trpc1" "Pla2g4a" "Dynll1" "Rab3a"
## [8] "Anxa2"
##
## $`cellular response to chemical stress`
## [1] "Ptgs2" "Hspb1" "Fos" "Rhob" "Hspa8" "Jun" "Lcn2"
##
## $`regulation of lens fiber cell differentiation`
## [1] "Cdkn1c" "Spry1"
##
## $`response to phorbol 13-acetate 12-myristate`
## [1] "Fos" "Btg2"
##
## $`cellular response to phorbol 13-acetate 12-myristate`
## [1] "Fos" "Btg2"
##
## $`keratinocyte differentiation`
## [1] "Ptgs2" "Etv4" "Sfn" "Zfp36" "Mafb"
##
## $`regulation of regulatory T cell differentiation`
## [1] "Hspb1" "Bcl6" "Irf1"
##
## $`amide metabolic process`
## [1] "Degs2" "Aldob" "Hap1" "Gstp1" "Arg2" "Acer2" "Clu" "Pmvk"
##
## $`cellular response to oxidative stress`
## [1] "Hspb1" "Fos" "Rhob" "Hspa8" "Jun" "Lcn2"
##
## $`maternal placenta development`
## [1] "Ptgs2" "Junb" "Pla2g4a"
##
## $`negative regulation of chemotaxis`
## [1] "Dusp1" "Gstp1" "Robo2"
##
## $`positive regulation of release of sequestered calcium ion into cytosol`
## [1] "Hap1" "Trpc1" "Cx3cl1"
##
## $`regulation of animal organ morphogenesis`
## [1] "Bmp2" "Wnt10a" "Spry1" "Robo2"
##
## $`positive regulation of phosphatase activity`
## [1] "Chp2" "Bmp2"
##
## $`regulation of microtubule nucleation`
## [1] "Hspa1a" "Hspa1b"
##
## $`regulation of fever generation`
## [1] "Ptgs2" "Ptges"
##
## $`negative regulation of erythrocyte differentiation`
## [1] "Zfp36" "Mafb"
##
## $`positive regulation of unsaturated fatty acid biosynthetic process`
## [1] "Ptgs2" "Pla2g4a"
##
## $`response to temperature stimulus`
## [1] "Ptgs2" "Hspb1" "Hspa1a" "Hspa1b" "Hspa8"
##
## $`positive regulation of lipid transport`
## [1] "Ptges" "Lipg" "Pla2g4a" "Anxa2"
##
## $`negative regulation of lymphocyte activation`
## [1] "Hspb1" "Bcl6" "Hfe" "Irf1" "Arg2"
##
## $`cellular response to epidermal growth factor stimulus`
## [1] "Fos" "Zfp36" "Gstp1"
##
## $`response to mechanical stimulus`
## [1] "Ptgs2" "Fos" "Btg2" "F11r" "Jun" "Irf1"
##
## $`regulation of endothelial cell migration`
## [1] "Ptgs2" "Hspb1" "Rhob" "Bmper" "Lcn2"
##
## $`regulation of organic acid transport`
## [1] "Ptges" "Rgs2" "Pla2g4a" "Arg2"
##
## $`regulatory T cell differentiation`
## [1] "Hspb1" "Bcl6" "Irf1"
##
## $`regulation of prostaglandin biosynthetic process`
## [1] "Ptgs2" "Pla2g4a"
##
## $`cortisol metabolic process`
## [1] "Bmp2" "Hsd11b2"
##
## $`macrophage proliferation`
## [1] "Clu" "Cx3cl1"
##
## $`chaperone-mediated autophagy`
## [1] "Hspa8" "Clu"
##
## $`positive regulation of non-motile cilium assembly`
## [1] "Hap1" "Dynll1"
##
## $`negative regulation of MAPK cascade`
## [1] "Dusp1" "Bmp2" "Rgs2" "Spry1" "Gstp1"
##
## $`alcohol metabolic process`
## [1] "Degs2" "Bmp2" "Pla2g4a" "Acer2" "Hsd11b2" "Pmvk" "Ttc39b"
##
## $`response to corticosteroid`
## [1] "Ptgs2" "Fos" "Zfp36" "Gstp1" "Hsd11b2"
##
## $`regulation of neurogenesis`
## [1] "Ptprz1" "Ache" "Btg2" "Bmp2" "Hap1" "Robo2" "Anxa2" "Cx3cl1"
##
## $`positive regulation of transmembrane receptor protein serine/threonine kinase signaling pathway`
## [1] "Cdkn1c" "Bmp2" "Hfe" "Bmper"
##
## $`cell-substrate adhesion`
## [1] "Ptprz1" "Frem1" "Bcl6" "Limch1" "Cspg5" "Acer2" "Anxa2"
##
## $`response to BMP`
## [1] "Bmp2" "Bambi" "Hfe" "Bmper" "Vstm2a"
##
## $`cellular response to BMP stimulus`
## [1] "Bmp2" "Bambi" "Hfe" "Bmper" "Vstm2a"
##
## $`leukocyte proliferation`
## [1] "Junb" "Bcl6" "Irf1" "Gstp1" "Arg2" "Clu" "Cx3cl1"
##
## $`response to endoplasmic reticulum stress`
## [1] "Manf" "Jun" "Hspa5" "Nrbf2" "Ppp1r15a" "Clu"
##
## $`carboxylic acid transport`
## [1] "Ptgs2" "Ptges" "Rgs2" "Slc6a7" "Pla2g4a" "Arg2" "Slco4a1"
##
## $`organelle fusion`
## [1] "Syt5" "Cav2" "Pla2g4a" "Rab3a" "Anxa2"
##
## $`positive regulation of dephosphorylation`
## [1] "Chp2" "Bmp2"
##
## $`positive regulation of nuclear-transcribed mRNA poly(A) tail shortening`
## [1] "Btg2" "Zfp36"
##
## $`microglial cell activation`
## [1] "Jun" "Clu" "Cx3cl1"
##
## $`acute-phase response`
## [1] "Ptgs2" "Ptges" "Hfe"
##
## $`type 2 immune response`
## [1] "Bcl6" "Irf1" "Arg2"
##
## $`regulation of erythrocyte differentiation`
## [1] "Hspa1b" "Zfp36" "Mafb"
##
## $`organic acid transport`
## [1] "Ptgs2" "Ptges" "Rgs2" "Slc6a7" "Pla2g4a" "Arg2" "Slco4a1"
##
## $`mitotic nuclear division`
## [1] "Cep85" "Dusp1" "Cdkn1c" "Cav2" "Hspa1a" "Hspa1b"
##
## $`response to xenobiotic stimulus`
## [1] "Ptgs2" "Fos" "Hspa8" "Jun" "Lcn2" "Gstp1" "Acer2"
## [8] "Hsd11b2"
##
## $`response to epidermal growth factor`
## [1] "Fos" "Zfp36" "Gstp1"
##
## $`regulation of cyclin-dependent protein kinase activity`
## [1] "Cdkn1c" "Sfn" "Cdk5rap1"
##
## $`positive regulation of endothelial cell migration`
## [1] "Ptgs2" "Hspb1" "Rhob" "Lcn2"
##
## $`regulation of calcium ion transmembrane transport`
## [1] "Mcub" "Hap1" "Trpc1" "Cacna2d1" "Cx3cl1"
##
## $`receptor-mediated endocytosis`
## [1] "Ache" "Cav2" "Hfe" "Hap1" "Clu" "Anxa2"
##
## $`unsaturated fatty acid biosynthetic process`
## [1] "Ptgs2" "Ptges" "Pla2g4a"
##
## $`icosanoid biosynthetic process`
## [1] "Ptgs2" "Ptges" "Pla2g4a"
##
## $`olefinic compound metabolic process`
## [1] "Ptgs2" "Bmp2" "Pla2g4a" "Gstp1" "Hsd11b2"
##
## $`fever generation`
## [1] "Ptgs2" "Ptges"
##
## $`membrane raft assembly`
## [1] "Cav2" "Anxa2"
##
## $`regulation of iron ion transport`
## [1] "Hfe" "Lcn2"
##
## $`regulation of T-helper 2 cell differentiation`
## [1] "Bcl6" "Irf1"
##
## $`response to parathyroid hormone`
## [1] "Fos" "Cited1"
##
## $`positive regulation of glial cell migration`
## [1] "Ptprz1" "Cx3cl1"
##
## $`regulation of unsaturated fatty acid biosynthetic process`
## [1] "Ptgs2" "Pla2g4a"
##
## $`regulation of leukocyte cell-cell adhesion`
## [1] "Hspb1" "Bcl6" "Cd83" "Hfe" "Irf1" "Gstp1" "Arg2"
##
## $`regulation of calcium ion transport`
## [1] "Mcub" "Ptgs2" "Hap1" "Trpc1" "Cacna2d1" "Cx3cl1"
##
## $`muscle organ development`
## [1] "Mcub" "Fos" "Btg2" "Cav2" "Bmp2" "Hspa8" "Mymx"
##
## $`negative regulation of defense response`
## [1] "Sfn" "Zfp36" "Ier3" "Gstp1" "Arg2" "Cx3cl1"
##
## $`leukocyte activation involved in inflammatory response`
## [1] "Jun" "Clu" "Cx3cl1"
##
## $`placenta development`
## [1] "Ptgs2" "Junb" "Cdkn1c" "Pla2g4a" "Cited1"
##
## $`positive regulation of myeloid cell differentiation`
## [1] "Fos" "Hspa1b" "Klf10" "Jun"
##
## $`temperature homeostasis`
## [1] "Ptgs2" "Ache" "Ptges" "Ksr2" "Lcn2"
##
## $`regulation of smooth muscle cell proliferation`
## [1] "Ptgs2" "Bmp2" "Jun" "Gstp1" "Cx3cl1"
##
## $`icosanoid secretion`
## [1] "Ptgs2" "Ptges" "Pla2g4a"
##
## $`cellular response to heat`
## [1] "Ptgs2" "Hspa1b" "Hspa8"
##
## $`response to cadmium ion`
## [1] "Fos" "Hspa8" "Jun"
##
## $`positive regulation of prostaglandin secretion`
## [1] "Ptges" "Pla2g4a"
##
## $`regulation of odontogenesis of dentin-containing tooth`
## [1] "Bmp2" "Wnt10a"
##
## $`regulation of nuclear-transcribed mRNA poly(A) tail shortening`
## [1] "Btg2" "Zfp36"
##
## $`regulation of small molecule metabolic process`
## [1] "Igfbp4" "Ptgs2" "Bmp2" "Aldob" "Ier3" "Pla2g4a" "Ttc39b"
##
## $`negative regulation of T cell differentiation`
## [1] "Hspb1" "Bcl6" "Irf1"
##
## $`cellular response to starvation`
## [1] "Fos" "Hfe" "Klf10" "Jun" "Hspa5"
##
## $`regulation of intracellular transport`
## [1] "Ptgs2" "Chp2" "Sfn" "Hap1" "Ier3" "Anxa2"
##
## $`regulation of epidermal cell differentiation`
## [1] "Etv4" "Sfn" "Zfp36"
##
## $`positive regulation of blood pressure`
## [1] "F11r" "Manf" "Hsd11b2"
##
## $`amino acid import across plasma membrane`
## [1] "Rgs2" "Slc6a7" "Arg2"
##
## $`positive regulation of miRNA transcription`
## [1] "Fos" "Bmp2" "Jun"
##
## $`alpha-beta T cell activation`
## [1] "Bcl6" "Cd83" "Hfe" "Irf1" "Arg2"
##
## $`fatty acid transport`
## [1] "Ptgs2" "Ptges" "Pla2g4a" "Slco4a1"
##
## $`regulation of non-motile cilium assembly`
## [1] "Hap1" "Dynll1"
##
## $`regulation of interleukin-1 production`
## [1] "Hspb1" "Gstp1" "Arg2" "Cx3cl1"
##
## $`negative regulation of leukocyte differentiation`
## [1] "Hspb1" "Bcl6" "Irf1" "Mafb"
##
## $`negative regulation of cell cycle`
## [1] "Ptgs2" "Dusp1" "Cdkn1c" "Bmp2" "Rhob" "Cdk5rap1" "Ier3"
##
## $`smooth muscle cell proliferation`
## [1] "Ptgs2" "Bmp2" "Jun" "Gstp1" "Cx3cl1"
##
## $`membrane assembly`
## [1] "Cav2" "Anxa2" "Mafb"
##
## $`response to insulin`
## [1] "Ache" "Fos" "Cav2" "Gstp1" "Cited1" "Hsd11b2"
##
## $`regulation of fibroblast proliferation`
## [1] "Ptprz1" "Jun" "Gstp1" "Anxa2"
##
## $`axon regeneration`
## [1] "Scarf1" "Jun" "Cspg5"
##
## $`p38MAPK cascade`
## [1] "Dusp1" "Bmp2" "Zfp36"
##
## $`glial cell activation`
## [1] "Jun" "Clu" "Cx3cl1"
##
## $`heart field specification`
## [1] "Bmp2" "Robo2"
##
## $`regulation of translational fidelity`
## [1] "Cdk5rap1" "Lars2"
##
## $`regulation of heat generation`
## [1] "Ptgs2" "Ptges"
##
## $`regulation of prostaglandin secretion`
## [1] "Ptges" "Pla2g4a"
##
## $`positive regulation of brown fat cell differentiation`
## [1] "Ptgs2" "Vstm2a"
##
## $`regulation of plasma membrane organization`
## [1] "Rab3a" "Anxa2"
##
## $`lipid export from cell`
## [1] "Ptgs2" "Ptges" "Pla2g4a"
##
## $`regulation of proteasomal ubiquitin-dependent protein catabolic process`
## [1] "Hspa1a" "Hspa1b" "Hfe" "Clu"
##
## $`interleukin-1 production`
## [1] "Hspb1" "Gstp1" "Arg2" "Cx3cl1"
##
## $`negative regulation of hemopoiesis`
## [1] "Hspb1" "Bcl6" "Irf1" "Mafb"
##
## $`negative regulation of cell-substrate adhesion`
## [1] "Ptprz1" "Bcl6" "Acer2"
##
## $`regulation of macrophage activation`
## [1] "Mcub" "Pla2g4a" "Cx3cl1"
##
## $`regulation of CD4-positive, alpha-beta T cell differentiation`
## [1] "Bcl6" "Cd83" "Irf1"
##
## $`regulation of synaptic vesicle exocytosis`
## [1] "Syt5" "Cspg5" "Rab3a"
##
## $`positive regulation of DNA-binding transcription factor activity`
## [1] "Bmp2" "Hspa1b" "Traf1" "Bex2" "Clu"
##
## $`regulation of protein ubiquitination`
## [1] "Arrdc4" "Hspa1b" "Nsmce3" "Bex2" "Hspa5"
##
## $`lysosomal transport`
## [1] "Hspa1a" "Rhob" "Hspa8" "Clu"
##
## $`glycine transport`
## [1] "Rgs2" "Slc6a7"
##
## $`negative regulation of smooth muscle contraction`
## [1] "Ptgs2" "Rgs2"
##
## $`positive regulation of receptor-mediated endocytosis`
## [1] "Hfe" "Clu" "Anxa2"
##
## $`brown fat cell differentiation`
## [1] "Ptgs2" "Rgs2" "Vstm2a"
##
## $`positive regulation of miRNA metabolic process`
## [1] "Fos" "Bmp2" "Jun"
##
## $`negative regulation of immune response`
## [1] "Bcl6" "Sfn" "Hfe" "Irf1" "Arg2"
##
## $`skeletal muscle tissue development`
## [1] "Mcub" "Fos" "Btg2" "Cav2" "Hspa8"
##
## $`positive regulation of epithelial cell differentiation`
## [1] "Etv4" "Bmp2" "Sfn"
##
## $`regulation of sterol transport`
## [1] "Lipg" "Anxa2" "Ttc39b"
##
## $`regulation of cholesterol transport`
## [1] "Lipg" "Anxa2" "Ttc39b"
##
## $`negative regulation of lymphocyte differentiation`
## [1] "Hspb1" "Bcl6" "Irf1"
##
## $`regulation of epidermis development`
## [1] "Etv4" "Sfn" "Zfp36"
##
## $`regulation of exocytosis`
## [1] "Syt5" "Hap1" "Cspg5" "Rab3a" "Anxa2"
##
## $`morphogenesis of an endothelium`
## [1] "Rhob" "Lcn2"
##
## $`endothelial tube morphogenesis`
## [1] "Rhob" "Lcn2"
##
## $`negative regulation of amyloid-beta formation`
## [1] "Hap1" "Clu"
##
## $`monocarboxylic acid biosynthetic process`
## [1] "Ptgs2" "Ptges" "Lipg" "Pla2g4a" "Gstp1"
##
## $`CD4-positive, alpha-beta T cell activation`
## [1] "Bcl6" "Cd83" "Irf1" "Arg2"
##
## $`regulation of nucleocytoplasmic transport`
## [1] "Ptgs2" "Chp2" "Sfn" "Ier3"
##
## $`regulation of blood pressure`
## [1] "Ptgs2" "F11r" "Manf" "Ier3" "Hsd11b2"
##
## $`small GTPase-mediated signal transduction`
## [1] "Bcl6" "Rhob" "F11r" "Spry1" "Dynlt1f" "Ksr2" "Dock10"
##
## $`positive regulation of neurogenesis`
## [1] "Ptprz1" "Ache" "Bmp2" "Hap1" "Robo2" "Cx3cl1"
##
## $`regulation of ERK1 and ERK2 cascade`
## [1] "Dusp1" "Bmp2" "Spry1" "Bmper" "Jun" "Gstp1"
##
## $`positive regulation of transforming growth factor beta production`
## [1] "Ptgs2" "Cx3cl1"
##
## $`membrane biogenesis`
## [1] "Cav2" "Anxa2" "Mafb"
##
## $`cell-cell adhesion via plasma-membrane adhesion molecules`
## [1] "Bmp2" "Scarf1" "Pcdh1" "Robo2" "Cx3cl1"
##
## $`bone mineralization`
## [1] "Ptgs2" "Bmp2" "Tent5a" "Klf10"
##
## $`regulation of receptor-mediated endocytosis`
## [1] "Hfe" "Hap1" "Clu" "Anxa2"
##
## $`regulation of cell-substrate adhesion`
## [1] "Ptprz1" "Bcl6" "Limch1" "Cspg5" "Acer2"
##
## $`regulation of chemotaxis`
## [1] "Hspb1" "Dusp1" "Gstp1" "Robo2" "Cx3cl1"
##
## $`positive regulation of proteolysis`
## [1] "Hspa1a" "Hspa1b" "Hspa8" "Acer2" "Clu" "Anxa2"
##
## $`negative regulation of tumor necrosis factor production`
## [1] "Gstp1" "Arg2" "Cx3cl1"
##
## $`regulation of monoatomic cation transmembrane transport`
## [1] "Mcub" "Hap1" "Trpc1" "Lcn2" "Cacna2d1" "Cx3cl1"
##
## $`regulation of amino acid import across plasma membrane`
## [1] "Rgs2" "Arg2"
##
## $`negative regulation of mitochondrial membrane permeability`
## [1] "Dynlt1f" "Ier3"
##
## $`T-helper 2 cell differentiation`
## [1] "Bcl6" "Irf1"
##
## $`regulation of receptor binding`
## [1] "Hfe" "Anxa2"
##
## $`negative regulation of amyloid precursor protein catabolic process`
## [1] "Hap1" "Clu"
##
## $`regulation of amino acid transmembrane transport`
## [1] "Rgs2" "Arg2"
##
## $`regulation of CD8-positive, alpha-beta T cell activation`
## [1] "Hfe" "Irf1"
##
## $`endothelial cell migration`
## [1] "Ptgs2" "Hspb1" "Rhob" "Bmper" "Lcn2"
##
## $`lipid transport`
## [1] "Ptgs2" "Ptges" "Lipg" "Pla2g4a" "Slco4a1" "Anxa2" "Ttc39b"
##
## $`protein dephosphorylation`
## [1] "Ptprz1" "Dusp1" "Ppm1j" "Ppp1r15a"
##
## $`neuron projection regeneration`
## [1] "Scarf1" "Jun" "Cspg5"
##
## $`negative regulation of tumor necrosis factor superfamily cytokine production`
## [1] "Gstp1" "Arg2" "Cx3cl1"
##
## $`cell-matrix adhesion`
## [1] "Frem1" "Bcl6" "Limch1" "Acer2" "Anxa2"
##
## $`positive regulation by host of viral process`
## [1] "Cav2" "Hspa8"
##
## $`sphingoid metabolic process`
## [1] "Degs2" "Acer2"
##
## $`regulation of protein-containing complex assembly`
## [1] "Hspa1a" "Hspa1b" "Hspa8" "Hspa5" "Rab3a" "Capg" "Clu"
##
## $`regulation of small GTPase mediated signal transduction`
## [1] "Bcl6" "F11r" "Spry1" "Dynlt1f" "Dock10"
##
## $`regulation of amide metabolic process`
## [1] "Aldob" "Hap1" "Clu"
##
## $`regulation of SMAD protein signal transduction`
## [1] "Bmp2" "Hfe" "Bmper"
##
## $`regulation of fat cell differentiation`
## [1] "Ptgs2" "Bmp2" "Zfp36" "Vstm2a"
##
## $`positive regulation of binding`
## [1] "Bmp2" "Bambi" "Hfe" "Anxa2"
##
## $`skin development`
## [1] "Ptgs2" "Etv4" "Sfn" "Wnt10a" "Zfp36" "Mafb"
##
## $`animal organ formation`
## [1] "Bmp2" "Spry1" "Robo2"
##
## $`regulation of lipoprotein particle clearance`
## [1] "Lipg" "Anxa2"
##
## $`negative regulation of amide metabolic process`
## [1] "Hap1" "Clu"
##
## $`regulation of mitotic spindle assembly`
## [1] "Hspa1a" "Hspa1b"
##
## $`tertiary alcohol metabolic process`
## [1] "Bmp2" "Hsd11b2"
##
## $`negative regulation of membrane permeability`
## [1] "Dynlt1f" "Ier3"
##
## $`regulation of adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains`
## [1] "Bcl6" "Hspa8" "Hfe" "Pla2g4a" "Irf1"
##
## $`regulation of myeloid leukocyte differentiation`
## [1] "Fos" "Klf10" "Jun" "Mafb"
##
## $`fibroblast proliferation`
## [1] "Ptprz1" "Jun" "Gstp1" "Anxa2"
##
## $`calcium ion transport`
## [1] "Mcub" "Ptgs2" "Hap1" "Tmem37" "Trpc1" "Cacna2d1" "Cx3cl1"
##
## $`regulation of nitric oxide biosynthetic process`
## [1] "Ptgs2" "Dynll1" "Clu"
##
## $`cellular response to hydrogen peroxide`
## [1] "Rhob" "Hspa8" "Lcn2"
##
## $`learning or memory`
## [1] "Ptprz1" "Ptgs2" "Fos" "Btg2" "Jun" "Lcn2"
##
## $`extrinsic apoptotic signaling pathway`
## [1] "Hspa1b" "Traf1" "Lcn2" "Gstp1" "Cx3cl1"
##
## $`positive regulation of myeloid leukocyte differentiation`
## [1] "Fos" "Klf10" "Jun"
##
## $`positive regulation of nucleocytoplasmic transport`
## [1] "Ptgs2" "Chp2" "Sfn"
##
## $`extrinsic apoptotic signaling pathway in absence of ligand`
## [1] "Hspa1b" "Lcn2" "Cx3cl1"
##
## $`regulation of miRNA transcription`
## [1] "Fos" "Bmp2" "Jun"
##
## $`icosanoid metabolic process`
## [1] "Ptgs2" "Ptges" "Pla2g4a" "Gstp1"
##
## $`positive regulation of intracellular transport`
## [1] "Ptgs2" "Chp2" "Sfn" "Anxa2"
##
## $`organic anion transport`
## [1] "Ptgs2" "Ptges" "Rgs2" "Slc6a7" "Pla2g4a" "Arg2" "Slco4a1"
##
## $`positive regulation of icosanoid secretion`
## [1] "Ptges" "Pla2g4a"
##
## $`response to muscle stretch`
## [1] "Fos" "Jun"
##
## $`regulation of odontogenesis`
## [1] "Bmp2" "Wnt10a"
##
## $`positive regulation of epidermal cell differentiation`
## [1] "Etv4" "Sfn"
##
## $`negative regulation of T-helper cell differentiation`
## [1] "Bcl6" "Irf1"
##
## $`negative regulation of cyclin-dependent protein kinase activity`
## [1] "Cdkn1c" "Cdk5rap1"
##
## $`negative regulation of locomotion`
## [1] "Dusp1" "Rhob" "Limch1" "Gstp1" "Robo2" "Cx3cl1"
##
## $`positive regulation of proteasomal ubiquitin-dependent protein catabolic process`
## [1] "Hspa1a" "Hspa1b" "Clu"
##
## $`positive regulation of fibroblast proliferation`
## [1] "Ptprz1" "Jun" "Anxa2"
##
## $`L-alpha-amino acid transmembrane transport`
## [1] "Rgs2" "Slc6a7" "Arg2"
##
## $`calcium ion transmembrane transport`
## [1] "Mcub" "Hap1" "Tmem37" "Trpc1" "Cacna2d1" "Cx3cl1"
##
## $`negative regulation of growth`
## [1] "Bcl6" "Hspa1a" "Rgs2" "Hspa1b" "Wwc2"
##
## $`organic hydroxy compound biosynthetic process`
## [1] "Bmp2" "Trpc1" "Cited1" "Acer2" "Pmvk"
##
## $`ERK1 and ERK2 cascade`
## [1] "Dusp1" "Bmp2" "Spry1" "Bmper" "Jun" "Gstp1"
##
## $`unsaturated fatty acid metabolic process`
## [1] "Ptgs2" "Ptges" "Pla2g4a" "Gstp1"
##
## $`signal transduction in absence of ligand`
## [1] "Hspa1b" "Lcn2" "Cx3cl1"
##
## $`miRNA transcription`
## [1] "Fos" "Bmp2" "Jun"
##
## $`regulation of nitric oxide metabolic process`
## [1] "Ptgs2" "Dynll1" "Clu"
##
## $`regulation of protein modification by small protein conjugation or removal`
## [1] "Arrdc4" "Hspa1b" "Nsmce3" "Bex2" "Hspa5"
##
## $`vascular process in circulatory system`
## [1] "Ptgs2" "Rgs2" "C2cd4b" "Manf" "Cx3cl1"
##
## $`regulation of phosphatase activity`
## [1] "Chp2" "Bmp2"
##
## $`calcium-independent cell-cell adhesion via plasma membrane cell-adhesion molecules`
## [1] "Bmp2" "Cx3cl1"
##
## $`melanin biosynthetic process`
## [1] "Trpc1" "Cited1"
##
## $`regulation of insulin-like growth factor receptor signaling pathway`
## [1] "Igfbp4" "Bmp2"
##
## $`nucleocytoplasmic transport`
## [1] "Ptgs2" "Chp2" "Sfn" "Hspa8" "Ier3" "Cited1"
##
## $`nuclear transport`
## [1] "Ptgs2" "Chp2" "Sfn" "Hspa8" "Ier3" "Cited1"
##
## $`regulation of alpha-beta T cell differentiation`
## [1] "Bcl6" "Cd83" "Irf1"
##
## $`regulation of post-translational protein modification`
## [1] "Arrdc4" "Hspa1b" "Nsmce3" "Bex2" "Hspa5"
##
## $`positive regulation of cation transmembrane transport`
## [1] "Hap1" "Trpc1" "Lcn2" "Cx3cl1"
##
## $`regulation of reactive oxygen species metabolic process`
## [1] "Ier3" "Lcn2" "Gstp1" "Arg2"
##
## $`epidermal cell differentiation`
## [1] "Ptgs2" "Etv4" "Sfn" "Zfp36" "Mafb"
##
## $`regulation of glial cell migration`
## [1] "Ptprz1" "Cx3cl1"
##
## $`regulation of protein catabolic process`
## [1] "Hspa1a" "Hspa1b" "Hfe" "Ier3" "Clu" "Anxa2"
##
## $`maintenance of location`
## [1] "Hap1" "Vstm2a" "Trpc1" "Hspa5" "Cx3cl1" "Ttc39b"
##
## $`regulation of osteoblast differentiation`
## [1] "Bmp2" "Tent5a" "Bambi" "Cited1"
##
## $`regulation of adaptive immune response`
## [1] "Bcl6" "Hspa8" "Hfe" "Pla2g4a" "Irf1"
##
## $`modulation by host of symbiont process`
## [1] "Cav2" "Hspa8" "Jun"
##
## $`regulation of monoatomic ion transmembrane transport`
## [1] "Mcub" "Hap1" "Trpc1" "Lcn2" "Cacna2d1" "Cx3cl1"
##
## $`mRNA catabolic process`
## [1] "Btg2" "Hspa1a" "Tent5a" "Hspa1b" "Zfp36"
##
## $`regulation of Rho protein signal transduction`
## [1] "Bcl6" "F11r" "Dock10"
##
## $`regulation of release of sequestered calcium ion into cytosol`
## [1] "Hap1" "Trpc1" "Cx3cl1"
##
## $`cell recognition`
## [1] "Ptprz1" "Fetub" "Hspa1b" "Robo2"
##
## $`nuclear-transcribed mRNA poly(A) tail shortening`
## [1] "Btg2" "Zfp36"
##
## $`positive regulation of systemic arterial blood pressure`
## [1] "Manf" "Hsd11b2"
##
## $`melanin metabolic process`
## [1] "Trpc1" "Cited1"
##
## $`glucocorticoid metabolic process`
## [1] "Bmp2" "Hsd11b2"
##
## $`skeletal muscle cell proliferation`
## [1] "Fos" "Cav2"
##
## $`regulation of synaptic vesicle fusion to presynaptic active zone membrane`
## [1] "Syt5" "Rab3a"
##
## $`secondary metabolite biosynthetic process`
## [1] "Trpc1" "Cited1"
##
## $`regulation of brown fat cell differentiation`
## [1] "Ptgs2" "Vstm2a"
##
## $`regulation of synaptic vesicle membrane organization`
## [1] "Syt5" "Rab3a"
##
## $`response to ethanol`
## [1] "Fos" "Rgs2" "Hspa8" "Gstp1"
##
## $`negative regulation of ERK1 and ERK2 cascade`
## [1] "Dusp1" "Spry1" "Gstp1"
##
## $`vacuolar transport`
## [1] "Hspa1a" "Rhob" "Hspa8" "Clu"
##
## $`regulation of ubiquitin-dependent protein catabolic process`
## [1] "Hspa1a" "Hspa1b" "Hfe" "Clu"
##
## $`erythrocyte differentiation`
## [1] "Bcl6" "Hspa1b" "Zfp36" "Mafb"
##
## $`negative regulation of protein-containing complex assembly`
## [1] "Hspa8" "Hspa5" "Capg" "Clu"
##
## $`negative regulation of epithelial cell proliferation`
## [1] "Cdkn1c" "Etv4" "Cav2" "Sfn"
##
## $`hormone metabolic process`
## [1] "Iyd" "Bmp2" "Hfe" "Slco4a1" "Cpq"
##
## $`endocardial cushion formation`
## [1] "Bmp2" "Robo2"
##
## $`protein targeting to lysosome`
## [1] "Hspa8" "Clu"
##
## $`membrane raft organization`
## [1] "Cav2" "Anxa2"
##
## $`peptidyl-tyrosine dephosphorylation`
## [1] "Ptprz1" "Dusp1"
##
## $`negative regulation of CD4-positive, alpha-beta T cell differentiation`
## [1] "Bcl6" "Irf1"
##
## $`positive regulation of fatty acid biosynthetic process`
## [1] "Ptgs2" "Pla2g4a"
##
## $`mitochondrion distribution`
## [1] "Hap1" "Dynll1"
##
## $`response to alcohol`
## [1] "Fos" "Btg2" "Rgs2" "Hspa8" "Gstp1" "Pmvk"
##
## $`BMP signaling pathway`
## [1] "Bmp2" "Bambi" "Hfe" "Bmper"
##
## $`fat cell differentiation`
## [1] "Ptgs2" "Bmp2" "Rgs2" "Zfp36" "Vstm2a"
##
## $`cellular response to nutrient levels`
## [1] "Fos" "Hfe" "Klf10" "Jun" "Hspa5"
##
## $`heat generation`
## [1] "Ptgs2" "Ptges"
##
## $`regulation of icosanoid secretion`
## [1] "Ptges" "Pla2g4a"
##
## $`positive regulation of epidermis development`
## [1] "Etv4" "Sfn"
##
## $`positive regulation of fatty acid transport`
## [1] "Ptges" "Pla2g4a"
##
## $`negative regulation of inflammatory response`
## [1] "Zfp36" "Ier3" "Gstp1" "Cx3cl1"
##
## $`nitric oxide biosynthetic process`
## [1] "Ptgs2" "Dynll1" "Clu"
##
## $`myeloid leukocyte activation`
## [1] "Mcub" "Jun" "Pla2g4a" "Clu" "Cx3cl1"
##
## $`regulation of extrinsic apoptotic signaling pathway`
## [1] "Hspa1b" "Traf1" "Gstp1" "Cx3cl1"
##
## $`regulation of receptor recycling`
## [1] "Ache" "Anxa2"
##
## $`diol metabolic process`
## [1] "Degs2" "Acer2"
##
## $`tissue regeneration`
## [1] "Mcub" "Mymx" "Cpq"3.2 Downregulation Pathway
# Arrange and filter DEGs
df <- type_markers %>% arrange(desc(avg_log2FC))
df2 <- df %>% filter(p_val_adj < 0.05)
DEG_list <- df2
markers1down <- DEG_list %>% rownames_to_column(var="SYMBOL")
ENTREZ_list <- bitr(
geneID = rownames(DEG_list),
fromType = "SYMBOL",
toType = "ENTREZID",
OrgDb = org.Mm.eg.db
)## 'select()' returned 1:1 mapping between keys and columns## Warning in bitr(geneID = rownames(DEG_list), fromType = "SYMBOL", toType =
## "ENTREZID", : 2.76% of input gene IDs are fail to map...markers1down <- ENTREZ_list %>% inner_join(markers1down, by = "SYMBOL")
markers1down <- markers1down %>% dplyr::filter(p_val_adj < 0.05)
pos.markers1down <- markers1down %>% dplyr::filter(avg_log2FC < 0) %>% arrange(desc(abs(avg_log2FC)))
pos.ranks1down <- pos.markers1down$ENTREZID[abs(pos.markers1down$avg_log2FC) > 0.4]
# GO enrichment for downregulated genes
pos_go1down <- enrichGO(
gene = pos.ranks1down,
OrgDb = org.Mm.eg.db,
ont = "BP",
readable = TRUE
)
pos_go1down## #
## # over-representation test
## #
## #...@organism Mus musculus
## #...@ontology BP
## #...@keytype ENTREZID
## #...@gene chr [1:41] "268709" "54156" "18703" "15395" "27528" "14077" "12709" ...
## #...pvalues adjusted by 'BH' with cutoff <0.05
## #...32 enriched terms found
## 'data.frame': 32 obs. of 12 variables:
## $ ID : chr "GO:0070374" "GO:0070372" "GO:0090287" "GO:0061077" ...
## $ Description : chr "positive regulation of ERK1 and ERK2 cascade" "regulation of ERK1 and ERK2 cascade" "regulation of cellular response to growth factor stimulus" "chaperone-mediated protein folding" ...
## $ GeneRatio : chr "5/38" "5/38" "5/38" "3/38" ...
## $ BgRatio : chr "227/28928" "333/28928" "333/28928" "69/28928" ...
## $ RichFactor : num 0.022 0.015 0.015 0.0435 0.0138 ...
## $ FoldEnrichment: num 16.8 11.4 11.4 33.1 10.5 ...
## $ zScore : num 8.65 6.94 6.94 9.68 6.61 ...
## $ pvalue : num 1.16e-05 7.21e-05 7.21e-05 1.03e-04 1.07e-04 ...
## $ p.adjust : num 0.013 0.024 0.024 0.024 0.024 ...
## $ qvalue : num 0.00892 0.01644 0.01644 0.01644 0.01644 ...
## $ geneID : chr "Dusp15/Fgfbp3/Gas6/Notch2/Egf" "Dusp15/Fgfbp3/Gas6/Notch2/Egf" "Nrep/Fgf9/Fgfbp3/Sostdc1/Notch2" "Fkbp11/Umod/Pdcd5-ps" ...
## $ Count : int 5 5 5 3 5 5 2 2 4 2 ...
## #...Citation
## G Yu. Thirteen years of clusterProfiler. The Innovation. 2024, 5(6):100722# Visualization
chart1down <- dotplot(pos_go1down) +
ggtitle("type 1 downregulated control") +
theme_classic() +
theme(
plot.title = element_text(hjust = 0.5),
legend.position = "left",
axis.text.y = element_text(hjust = 0, size = 10)
) +
scale_y_discrete(
position = "right",
labels = function(x) str_wrap(x, width = 25)
)## Scale for y is already present.
## Adding another scale for y, which will replace the existing scale.
3.2.1 Downreg Gene View
pathway_type1down <- strsplit(pos_go1down$geneID, "/")
names(pathway_type1down) <- pos_go1down$Description
pathway_type1down## $`positive regulation of ERK1 and ERK2 cascade`
## [1] "Dusp15" "Fgfbp3" "Gas6" "Notch2" "Egf"
##
## $`regulation of ERK1 and ERK2 cascade`
## [1] "Dusp15" "Fgfbp3" "Gas6" "Notch2" "Egf"
##
## $`regulation of cellular response to growth factor stimulus`
## [1] "Nrep" "Fgf9" "Fgfbp3" "Sostdc1" "Notch2"
##
## $`chaperone-mediated protein folding`
## [1] "Fkbp11" "Umod" "Pdcd5-ps"
##
## $`ERK1 and ERK2 cascade`
## [1] "Dusp15" "Fgfbp3" "Gas6" "Notch2" "Egf"
##
## $`cell-substrate adhesion`
## [1] "Fam107a" "Egfl6" "Plau" "Plet1" "Gas6"
##
## $`intracellular chloride ion homeostasis`
## [1] "Ckb" "Umod"
##
## $`intracellular monoatomic anion homeostasis`
## [1] "Ckb" "Umod"
##
## $`regulation of cell-substrate adhesion`
## [1] "Fam107a" "Egfl6" "Plau" "Plet1"
##
## $`phosphatidylcholine biosynthetic process`
## [1] "Fabp3" "Fabp5"
##
## $`regulation of smooth muscle cell migration`
## [1] "Fgf9" "Plau" "Abhd2"
##
## $`regulation of transmembrane receptor protein serine/threonine kinase signaling pathway`
## [1] "Nrep" "Fgf9" "Sostdc1" "Notch2"
##
## $`chloride ion homeostasis`
## [1] "Ckb" "Umod"
##
## $`smooth muscle cell migration`
## [1] "Fgf9" "Plau" "Abhd2"
##
## $`plasminogen activation`
## [1] "Plau" "Pgk1"
##
## $`monoatomic anion homeostasis`
## [1] "Ckb" "Umod"
##
## $`activation of protein kinase B activity`
## [1] "Gas6" "Notch2"
##
## $`regulation of cell-matrix adhesion`
## [1] "Fam107a" "Plau" "Plet1"
##
## $`glomerular filtration`
## [1] "Umod" "Gas6"
##
## $`muscle cell migration`
## [1] "Fgf9" "Plau" "Abhd2"
##
## $`hepatocyte proliferation`
## [1] "Plau" "Notch2"
##
## $`epithelial cell proliferation involved in liver morphogenesis`
## [1] "Plau" "Notch2"
##
## $`embryonic limb morphogenesis`
## [1] "Hoxa10" "Fgf9" "Notch2"
##
## $`embryonic appendage morphogenesis`
## [1] "Hoxa10" "Fgf9" "Notch2"
##
## $`renal filtration`
## [1] "Umod" "Gas6"
##
## $`liver morphogenesis`
## [1] "Plau" "Notch2"
##
## $`negative regulation of cell-matrix adhesion`
## [1] "Fam107a" "Plet1"
##
## $`regulation of smooth muscle cell differentiation`
## [1] "Fgf9" "Notch2"
##
## $`negative regulation of proteolysis`
## [1] "Ide" "Plau" "Timp3" "Gas6"
##
## $`gland morphogenesis`
## [1] "Plau" "Sostdc1" "Notch2"
##
## $`transforming growth factor beta receptor superfamily signaling pathway`
## [1] "Nrep" "Fgf9" "Sostdc1" "Notch2"
##
## $`renal absorption`
## [1] "Umod" "Gas6"# Start filtering process here
# Maybe use genes you discover from Upset Plot
# Maybe try with subtypes fitler genes
gyarmati <- c("Fabp3", "Ccn1", "Foxq1", "Cxcl12", "Vash2", "Pamr1", "Vegfd", "Ccn3", "Bmp3", "Fgf9", "Spp1", "Wnt10a", "Sfrp1", "Tcf4", "Pappa2", "Unc5d", "Sema3c", "Robo2", "Slit2", "Egfl6", "Hgfac", "Pdgfc", "Megf9", "Frem1", "Thsd4", "Spock2", "Mmp14", "Adamtsl2", "Car8", "Irx1", "Irx2", "Hoxd11", "Hoxc4", "Etv1")
df3 <- type_markers %>%
filter(gene %in% gyarmati) %>%
arrange(desc(avg_log2FC))
df3 <- rownames(df3)
df <- AverageExpression(
object = SO4,
features = df3,
group.by = 'treatment'
)$RNA## As of Seurat v5, we recommend using AggregateExpression to perform pseudo-bulk analysis.
## Names of identity class contain underscores ('_'), replacing with dashes ('-')
## This message is displayed once per session.## 24 x 2 sparse Matrix of class "dgCMatrix"
## control low-salt
## Pappa2 6.531402e+35 1.297082e+66
## Frem1 6.671330e-01 3.182392e+00
## Wnt10a 1.405144e+01 7.786316e+01
## Robo2 6.880488e+15 1.192981e+20
## Hoxc4 8.287261e-01 1.074161e+00
## Megf9 1.417514e+02 6.069250e+03
## Irx1 5.092308e+16 3.253313e+20
## Etv1 2.188832e+01 6.456954e+01
## Irx2 2.387772e+10 5.763812e+09
## Bmp3 2.217383e+07 1.102390e+09
## Sfrp1 8.518389e+87 3.659043e+88
## Vegfd 3.173728e+00 5.141249e+00
## Hgfac 1.091375e+00 1.701657e+00
## Vash2 3.906250e+00 3.524595e+01
## Thsd4 3.156320e+02 1.557459e+02
## Spock2 8.782243e+01 8.666974e-01
## Adamtsl2 2.425374e+00 9.739461e+00
## Mmp14 2.903324e+00 4.851085e+00
## Pamr1 7.977601e+05 6.994911e+07
## Hoxd11 2.683656e+00 4.938132e+00
## Cxcl12 1.781695e+00 1.482061e+00
## Fgf9 7.308532e+04 4.224723e+06
## Fabp3 8.046356e+06 1.633769e+06
## Egfl6 1.319648e+01 3.037382e+00df <- as.data.frame(df)
df <- t(scale(t(df)))
# convert df to tidy format
# only use about 10-15 genes
df_tidy <- df %>%
as.data.frame() %>%
rownames_to_column(var = "Gene") %>%
pivot_longer(cols = -Gene, names_to = "treatment", values_to = "Expression")
# Graph with geom_tile
df_tidy$treatment <- factor(df_tidy$treatment, levels = c("control","low-salt"))
f4 <- ggplot(df_tidy, aes(x = treatment, y = Gene, fill = Expression)) +
geom_tile(color = "black", size = 0.2, width = 0.97, height = 0.90) + # Adds thin border and spacing between tiles
scale_fill_distiller(palette = "RdYlBu") +
theme_minimal() +
theme(
axis.text = element_text(size = 12, color = "black"),
axis.title = element_text(size = 14),
axis.ticks = element_blank(), # Removes tick marks
panel.grid = element_blank(), # Removes grid lines
legend.position = "bottom", # Centers the legend below the plot
legend.title = element_text(size = 14), # Increases legend title size
legend.text = element_text(size = 12) # Increases legend text size
) +
labs(x = "Cell Type", y = "Gene", fill = "Relative Expression")## Warning: Using `size` aesthetic for lines was deprecated in ggplot2 3.4.0.
## ℹ Please use `linewidth` instead.
## This warning is displayed once every 8 hours.
## Call `lifecycle::last_lifecycle_warnings()` to see where this warning was
## generated.
df3 <- type_markers %>%
filter(gene %in% gyarmati) %>%
arrange(desc(avg_log2FC))
df3 <- rownames(df3)
df <- AverageExpression(
object = SO4,
features = df3,
group.by = 'sample'
)$RNA
df## 24 x 4 sparse Matrix of class "dgCMatrix"
## SO1 SO4 SO3 SO2
## Pappa2 1.624997e+27 9.394787e+35 4.577074e+50 4.328080e+66
## Frem1 5.032261e-01 7.389903e-01 2.455748e+00 4.880402e+00
## Wnt10a 4.968846e+00 1.803328e+01 1.096020e+02 3.696514e+00
## Robo2 2.257493e+16 3.797770e+08 2.280856e+13 3.980717e+20
## Hoxc4 1.162726e+00 6.822996e-01 1.044906e+00 1.142524e+00
## Megf9 1.201802e+02 1.512083e+02 7.927695e+03 1.726471e+03
## Irx1 5.999075e+13 7.322160e+16 2.516864e+17 1.084971e+21
## Etv1 3.684967e+00 2.986872e+01 2.282637e+01 1.621142e+02
## Irx2 5.833102e+10 8.773306e+09 1.023481e+09 1.684093e+10
## Bmp3 5.780747e+07 6.551941e+06 3.438930e+08 2.874832e+09
## Sfrp1 2.794890e+88 3.417901e+78 5.224841e+88 1.153674e+84
## Vegfd 2.107406e+00 3.641206e+00 4.451030e+00 6.754140e+00
## Hgfac 1.714995e+00 8.179782e-01 1.470009e+00 2.242968e+00
## Vash2 2.142977e+00 4.679274e+00 7.986470e+00 9.894542e+01
## Thsd4 3.644712e+01 4.380274e+02 1.763989e+02 1.074844e+02
## Spock2 2.846748e-01 1.261992e+02 8.603720e-01 8.814787e-01
## Adamtsl2 2.292680e+00 2.483547e+00 8.617702e+00 1.236077e+01
## Mmp14 2.731674e+00 2.978576e+00 4.177641e+00 6.424778e+00
## Pamr1 2.401602e+06 9.463135e+04 5.502337e+07 1.048273e+08
## Hoxd11 4.309507e+00 1.970879e+00 4.240257e+00 6.568913e+00
## Cxcl12 4.084340e+00 7.722092e-01 9.820518e-01 2.650473e+00
## Fgf9 2.153550e+04 9.568490e+04 4.299888e+04 1.399650e+07
## Fabp3 1.983636e+07 2.877586e+06 2.183898e+06 3.482377e+05
## Egfl6 1.422648e+01 1.274492e+01 1.538748e+00 6.539362e+00df <- as.data.frame(df)
df <- t(scale(t(df)))
# convert df to tidy format
df_tidy <- df %>%
as.data.frame() %>%
rownames_to_column(var = "Gene") %>%
pivot_longer(cols = -Gene, names_to = "sample", values_to = "Expression")
# Graph with geom_tile
df_tidy$sample <- factor(df_tidy$sample, levels = c("SO1","SO4","SO2","SO3"))
f4 <- ggplot(df_tidy, aes(x = sample, y = Gene, fill = Expression)) +
geom_tile(color = "black", size = 0.2, width = 0.97, height = 0.90) + # Adds thin border and spacing between tiles
scale_fill_distiller(palette = "RdYlBu") +
theme_minimal() +
theme(
axis.text = element_text(size = 12, color = "black"),
axis.title = element_text(size = 14),
axis.ticks = element_blank(), # Removes tick marks
panel.grid = element_blank(), # Removes grid lines
legend.position = "bottom", # Centers the legend below the plot
legend.title = element_text(size = 14), # Increases legend title size
legend.text = element_text(size = 12) # Increases legend text size
) +
labs(x = "Sample", y = "Gyarmati Genes", fill = "Relative Expression")
f4
4 Grouping as Treatment groups
# 1. Create new sample groups
treatmentgroup <- df_tidy %>%
mutate(
sample = case_when(
sample %in% c("SO1", "SO4") ~ "SO1_SO4",
sample %in% c("SO2", "SO3") ~ "SO2_SO3"
)
) %>%
# 2. Sum (or use mean) of Expression within each group for each Gene
group_by(Gene, sample) %>%
summarize(Expression = mean(Expression), .groups = "drop") # Use mean() if you prefer averaging
treatmentgroup$sample <- factor(treatmentgroup$sample, levels = c("SO1_SO4", "SO2_SO3"))
f4_grouped <- ggplot(treatmentgroup, aes(x = sample, y = Gene, fill = Expression)) +
geom_tile(color = "black", size = 0.2, width = 0.97, height = 0.90) +
scale_fill_distiller(palette = "RdYlBu") +
theme_minimal() +
theme(
axis.text = element_text(size = 12, color = "black"),
axis.title = element_text(size = 14),
axis.ticks = element_blank(),
panel.grid = element_blank(),
legend.position = "bottom",
legend.title = element_text(size = 14),
legend.text = element_text(size = 12)
) +
labs(x = "Control Low Salt ", y = "Gyarmati Genes", fill = "Relative Expression")
f4_grouped
# HeatMap of each clusters top genes from pathway analysis
